Endoscopic and video capsule endoscopic observation of Yersinia enterocolitis

A woman in her late 20s suffered from epigastralgia following lower abdominal pain with diarrhea. Kampo medicine relieved the complaints, but the pain recurred a month later. She had immigrated from Vietnam to Japan 6 months before the onset of the abdominal pain. Blood test findings were almost within normal limits, except for mild C-reactive protein elevation and positive Helicobacter pylori antibody findings. Colonoscopy revealed an edematous cobblestone-like appearance at the end of the ileum with irregular ulceration mimicking Crohn's disease. Video capsule endoscopy was performed to detect lesions in the small intestine and demonstrated irregular ileal ulcer, reminiscent of Crohn's disease. A biopsy performed during colonoscopy demonstrated granulomatous inflammation with a moderate accumulation of plasma cells and mononuclear cells. The bacterial culture of the biopsy specimen proved the growth of Yersinia enterocolitica. Levofloxacin 500 mg for 7 days rapidly relieved abdominal pain. Yersinia enterocolitis is rare in developed countries, but as a differential diagnosis for Crohn's disease, it is important to treat. This is the first case report of the video capsule endoscopy findings of Yersinia enterocolitis. Video capsule endoscopy can help to confirm the spread of the lesions of Yersinia enterocolitis.

Recognition of tRNA by aminoacyl-tRNA synthetase from hyperthermophilic archaea, Aeropyrum pernix K1

To study the recognition sites of tRNA for archaeal aminoacyl-tRNA synthetase, several aminoacyl-tRNA synthetase genes from hyperthermophilic archaeon, Aeropyrum pernix K1 were cloned and expressed. All the expressed enzymes showed extreme thermostability. Expressed threonyl-tRNA synthetase threonylated not only archaeal (A. pernix and Haloferax volcanii) threonine tRNAs but also Escherichia coli threonine tRNA. However, threonyl-tRNA synthetase from H. volcanii did not threonylate E. coli threonine tRNA.

Crystal structure of cobalt-containing nitrile hydratase

The crystal structure of cobalt-containing nitrile hydratase from Pseudonocardia thermophila JCM 3095 at 1.8 A resolution revealed the structure of the noncorrin cobalt at the catalytic center. Two cysteine residues (alphaCys(111) and alphaCys(113)) coordinated to the cobalt were posttranslationally modified to cysteine-sulfinic acid and to cysteine-sulfenic acid, respectively, like in iron-containing nitrile hydratase. A tryptophan residue (betaTrp(72)), which may be involved in substrate binding, replaced the tyrosine residue of iron-containing nitrile hydratase. The difference seems to be responsible for the preference for aromatic nitriles rather than aliphatic ones of cobalt-containing nitrile hydratase.

Role of a highly conserved YPITP motif in 2-oxoacid:ferredoxin oxidoreductase: heterologous expression of the gene from Sulfolobus sp.strain 7, and characterization of the recombinant and variant enzymes

2-Oxoacid:ferredoxin oxidoreductase from Sulfolobus sp. strain 7, an aerobic and thermoacidophilic crenoarchaeon, catalyses the coenzyme A-dependent oxidative decarboxylation of pyruvate and 2-oxoglutarate, a cognate Zn-7Fe-ferredoxin serving as an electron acceptor. It comprises two subunits, a (632 amino acids) and b (305 amino acids). To further elucidate its structure and function, we constructed a gene expression system. The wild-type recombinant enzyme was indistinguishable from the natural one in every criterion investigated. A series of variants was constructed to elucidate the role of the YPITP-motif (residues 253-257) in subunit a, which is conserved universally in the 2-oxoacid:ferredoxin oxidoreductase (OFOR) family. Single amino-acid replacements at Y253 and P257 by other amino acids caused a drastic loss of enzyme activity. T256, the hydroxyl group of which has been proposed to be essential for binding of the 2-oxo group of the substrate in the Desulfovibrio africanus enzyme, was unexpectedly replaceable with Ala, the kcat and Km for 2-oxoglutarate being approximately 33% and approximately 51%, respectively, as compared with that of the wild-type enzyme. Replacement at other positions resulted in a significant decrease in the kcat of the reaction while the Km for 2-oxoacid was only slightly affected. Thus, the YPITP-motif is essential for the turnover of the reaction rather than the affinity toward 2-oxoacid.

Identification of the catalytic residue of Thermococcus litoralis 4-alpha-glucanotransferase through mechanism-based labeling

Thermococcus litoralis 4-alpha-glucanotransferase (TLGT) belongs to family 57 of glycoside hydrolases and catalyzes the disproportionation and cycloamylose synthesis reactions. Family 57 glycoside hydrolases have not been well investigated, and even the catalytic mechanism involving the active site residues has not been studied. Using 3-ketobutylidene-beta-2-chloro-4-nitrophenyl maltopentaoside (3KBG5CNP) as a donor and glucose as an acceptor, we showed that the disproportionation reaction of TLGT involves a ping-pong bi-bi mechanism. On the basis of this reaction mechanism, the glycosyl-enzyme intermediate, in which a donor substrate was covalently bound to the catalytic nucleophile, was trapped by treating the enzyme with 3KBG5CNP in the absence of an acceptor and was detected by matrix-assisted laser desorption ionization time-of-flight mass spectrometry after peptic digestion. Postsource decay analysis suggested that either Glu-123 or Glu-129 was the catalytic nucleophile of TLGT. Glu-123 was completely conserved between family 57 enzymes, and the catalytic activity of the E123Q mutant enzyme was greatly decreased. On the other hand, Glu-129 was a variable residue, and the catalytic activity of the E129Q mutant enzyme was not decreased. These results indicate that Glu-123 is the catalytic nucleophile of TLGT. Sequence alignment of TLGT and family 38 enzymes (class II alpha-mannosidases) revealed that Glu-123 of TLGT corresponds to the nucleophilic aspartic acid residue of family 38 glycoside hydrolases, suggesting that family 57 and 38 glycoside hydrolases may have had a common ancestor.

Structural basis for the ADP-specificity of a novel glucokinase from a hyperthermophilic archaeon

BACKGROUND

ATP is the most common phosphoryl group donor for kinases. However, certain hyperthermophilic archaea such as Thermococcus litoralis and Pyrococcus furiosus utilize unusual ADP-dependent glucokinases and phosphofructokinases in their glycolytic pathways. These ADP-dependent kinases are homologous to each other but show no sequence similarity to any of the hitherto known ATP-dependent enzymes.

RESULTS

We solved the crystal structure at 2.3 A resolution of an ADP-dependent glucokinase from T. litoralis (tlGK) complexed with ADP. The overall structure can be divided into large and small alpha/beta domains, and the ADP molecule is buried in a shallow pocket in the large domain. Unexpectedly, the structure was similar to those of two ATP-dependent kinases, ribokinase and adenosine kinase. Comparison based on three-dimensional structure revealed that several motifs important both in structure and function are conserved, and the recognition of the alpha- and beta-phosphate of the ADP in the tlGK was almost identical with the recognition of the beta- and gamma-phosphate of ATP in these ATP-dependent kinases.

CONCLUSIONS

Noticeable points of our study are the first structure of ADP-dependent kinase, the structural similarity to members of the ATP-dependent ribokinase family, its rare nucleotide specificity caused by a shift in nucleotide binding position by one phosphate unit, and identification of the residues that discriminate ADP- and ATP-dependence. The strict conservation of the binding site for the terminal and adjacent phosphate moieties suggests a common ancestral origin of both the ATP- and ADP-dependent kinases.

Second transmembrane segment of FtsH plays a role in its proteolytic activity and homo-oligomerization

The FtsH (HflB) protein of Escherichia coli is a membrane-bound ATP-dependent zinc protease. The role(s) of the N-terminal membrane-anchoring region of FtsH were studied by fusion with a maltose-binding protein (MBP) at five different N-termini of FtsH. The MBP-FtsH fusions were expressed in the cytoplasm of E. coli, and were purified as soluble proteins. The four longer constructs, which have a second transmembrane segment and the C-terminal cytoplasmic region in common, retained ATP-dependent protease activity toward heat-shock transcription factor sigma(32), and were found to be homo-oligomers. In contrast, the shortest construct which has the C-terminal cytoplasmic region but not the second transmembrane segment showed neither protease activity nor oligomerization. Therefore, the second transmembrane segment, which neighbors the C-terminal cytoplasmic region of the FtsH, participates in not only its membrane-anchoring, but also its protease activity and homo-oligomerization.

High level expression of Thermococcus litoralis 4-alpha-glucanotransferase in a soluble form in Escherichia coli with a novel expression system involving minor arginine tRNAs and GroELS

The Thermococcus litoralis 4-alpha-glucanotransferase (GTase) gene has a high content of AGA and AGG codons for arginine, which are extremely rare in Escherichia coli. Expression of the GTase gene in E. coli resulted in low protein production and the accumulation of inclusion bodies. However, simultaneous expression of GTase with tRNA(AGA), tRNA(AGG) and GroELS affected both the production and solubility of GTase, and production of soluble GTase increasing about 5-fold. This new E. coli expression system should be applicable to the expression of not only archaeal but also eukaryotic genes, which usually contain a large number of AGA and AGG codons.

Weakly bound calcium ions involved in the thermostability of aqualysin I, a heat-stable subtilisin-type protease of Thermus aquaticus YT-1

Aqualysin I is a heat-stable protease; in the presence of 1 mM Ca(2+), the enzyme is stable at 80 degrees C and shows the highest activity at the same temperature. After gel filtration to remove free Ca(2+) from the purified enzyme sample, the enzyme (holo-aqualysin I) still bound Ca(2+) (1 mol/mol of the enzyme), but was no longer stable at 80 degrees C. On treatment of the holo-enzyme with EDTA, bound Ca(2+) decreased to about 0.3 mol/mol of the enzyme. The thermostability of holo-aqualysin I was dependent on the concentration of added Ca(2+), and 1 mM added Ca(2+) stabilized the enzyme completely, suggesting that aqualysin I has at least two Ca(2+) binding sites, i.e. stronger and weaker binding ones. Titration calorimetry showed single binding of Ca(2+) to the holo-enzyme with an association constant of 3.1 x 10(3) M(-1), and DeltaH and TDeltaS were calculated to be 2.3 and 6.9 kcal/mol, respectively, at 13 degrees C. La(3+), Sr(2+), Nd(3+), and Tb(3+) stabilized the holo-enzyme at 80 degrees C, as Ca(2+) did. These results suggest that the weaker binding site exhibits structural flexibility to bind several metal cations different in size and valency, and that the metal binding to the weaker binding site is essential for the thermostability of aqualysin I.

Zinc and an N-terminal extra stretch of the ferredoxin from a thermoacidophilic archaeon stabilize the molecule at high temperature

Ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7 has a 36-residue extra domain at its N-terminus and a 67-residue core domain carrying two iron-sulfur clusters. A zinc ion is held at the interface of the two domains through tetrahedral coordination of three histidine residues (-6, -19 and -34) and one aspartic acid residue (-76) [Fujii, T., Hata, Y., Oozeki, M., Moriyama, H., Wakagi, T., Tanaka, N. & Oshima, T. (1997) Biochemistry 36, 1505-1513]. To elucidate the roles of the novel zinc ion and the extra N-terminal domain, a series of truncated mutants was constructed: G1, V12, S17, G23, L31 and V38, which lack residues 0, 11, 16, 22, 30 and 37 starting from the N-terminus, respectively. A mutant with two histidine residues each replaced by an alanine residue, H16A/H19A, was also constructed. All the mutant ferredoxins had two iron-sulfur clusters, while zinc was retained only in G1 and V12. The thermal stability of the proteins was investigated by monitoring A408; the melting temperature (Tm) was approximately 109 degrees C for the natural ferredoxin, approximately 109 degrees C for G1, 97.6 degrees C for V12, 89.0 degrees C for S17, 89.2 degrees C for G23, 89.3 degrees C for L31, 82.1 degrees C for V38, and 89.4 degrees C for H16A/H19A. Km and Vmax values of 2-oxoglutarate:ferredoxin oxidoreductase for natural ferredoxin, G1, S17 and L31 were similar, suggesting that electron-accepting activities were not affected by the deletion. The combination of CD and fluorescent spectroscopic analyses with truncated mutant S17 indicated that not only the clusters but also the secondary and tertiary structures were simultaneously degraded at a Tm around 89 degrees C. These results unequivocally demonstrate that the zinc ion and certain parts, but not all, of the extra sequence stretch in the N-terminal domain are responsible not for function but for thermal stabilization of the molecule.

Cloning of the gene for inorganic pyrophosphatase from a thermoacidophilic archaeon, Sulfolobus sp. strain 7, and overproduction of the enzyme by coexpression of tRNA for arginine rare codon

The gene encoding an extremely stable inorganic pyrophosphatase from Sulfolobus sp. strain 7, a thermoacidophilic archaeon, was cloned and sequenced. An open reading frame consisted of 516 base pairs coding for a protein of 172-amino acid residues. The deduced sequence was supported by partial amino acid sequence analyses. All the catalytically important residues were conserved. A unique 17-base-pair sequence motif was found to be repeated four times in frame in the gene, encoding a cluster of acidic amino acids essential for the function. Although the codon usage of the gene was quite different from that of Escherichia coli, the gene was effectively expressed in E. coli. Coexpression of tRNA(Arg), cognate for the rare codon AGA in E. coli, however, further improved the production of the enzyme, which occupied more than 85% of the soluble proteins obtained after removal of heat denatured E. coli proteins.

Crystallographic and mutational analyses of an extremely acidophilic and acid-stable xylanase: biased distribution of acidic residues and importance of Asp37 for catalysis at low pH

Xylanase C from Aspergillus kawachii has an optimum pH of 2.0 and is stable at pH 1.0. The crystal structure of xylanase C was determined at 2.0 A resolution (R-factor = 19.4%). The overall structure was similar to those of other family 11 xylanases. Asp37 and an acid-base catalyst, Glu170, are located at a hydrogen-bonding distance (2.8 A), as in other xylanases with low pH optima. Asp37 of xylanase C was replaced with asparagine and other residues by site-directed mutagenesis. Analyses of the wild-type and mutant enzymes showed that Asp37 is important for high enzyme activity at low pH. In the case of the asparagine mutant, the optimum pH shifted to 5.0 and the maximum specific activity decreased to about 15% of that of the wild-type enzyme. On structural comparison with xylanases with higher pH optima, another striking feature of the xylanase C structure was found; the enzyme has numerous acidic residues concentrated on the surface (so-called 'Ser/Thr surface' in most family 11 xylanases). The relationship of the stability against extreme pH conditions and high salt concentrations with the spatially biased distribution of charged residues on the proteins is discussed.

Presence of Na(+)-stimulated V-type ATPase in the membrane of a facultatively anaerobic and halophilic alkaliphile

It was found that a facultatively anaerobic and halophilic alkaliphile, M-12 (Amphibacillus sp.), possesses a Na(+)-stimulated ATPase in the membrane. The ATPase activity was inhibited by NO3- and SCN- which are the inhibitors of V-type ATPase, but not by azide and vanadate, inhibitors of F-type ATPase and P-type ATPase, respectively. Upon the incubation of the membrane in buffer containing ATP and MgCl2, several polypeptides were released from the membrane. Among them, two major polypeptides with apparent molecular masses of 79 and 55 kDa crossreacted with an antiserum against the catalytic units (subunits A and B) of V-type ATPase from Enterococcus hirae. The N-terminal amino acid sequences of the 79 and 55 kDa polypeptides showed high similarity to those of subunits A and B of V-type ATPase from Enterococcus hirae, respectively. M-12 is likely to possess a V-type Na(+)-ATPase.

4-alpha-glucanotransferase from the hyperthermophilic archaeon Thermococcus litoralis--enzyme purification and characterization, and gene cloning, sequencing and expression in Escherichia coli

4-Alpha-Glucanotransferase was purified from cells of Thermococcus litoralis, a hyperthermophilic archaeon. The molecular mass of the enzyme was estimated to be approximately 87 kDa by gel filtration. The optimal temperature for its activity was 90 degrees C. The enzyme catalyzed the transglycosylation of maltooligosaccharides, yielding maltooligosaccharides of various lengths and glucose. When maltoheptaose was used as the substrate, glucoamylase-resistant and glucoamylase-sensitive saccharides were produced. On incubation of amylose with the T. litoralis enzyme, glucoamylase-resistant but alpha-amylase-sensitive molecules were produced, but the amount of reducing sugar showed only slight increases. These results indicate that the T. litoralis enzyme catalyzes not only intermolecular transglycosylation to produce linear alpha-1,4-glucan, but also intramolecular transglycosylation to produce cyclic alpha-1,4-glucan (cycloamylose), similarly to potato 4-alpha-glucanotransferase (called disproportionating enzyme). The gene encoding the T. litoralis 4-alpha-glucanotransferase was cloned, sequenced and expressed in Escherichia coli. The nucleotide sequence of the gene encoded a 659-amino acid protein with a calculated molecular mass of 77,883 Da. The amino acid sequence of the T. litoralis enzyme showed high similarity with those of alpha-amylases of Pyrococcus furiosus, a hyperthermophilic archaeon, and Dictyoglomus thermophilum, an extremely thermophilic bacterium, but little similarity with those of other known 4-alpha-glucanotransferases.

Increase of the protease activity of aqualysin I, a thermostable serine protease, by replacing Asn219 near the catalytic residue Ser222

Functional role of Asn219 of aqualysin I, a thermostable serine protease from Thermus aquaticus, was investigated by using site-directed mutagenesis. Replacement of Asn219 with serine increased the catalytic efficiency (kcat/Km) for synthetic peptide substrates about twice as much as that of the wild type, while threonine replacement caused a slight decrease in the efficiency. Such replacements resulted in a significant change of kcat rather than Km, indicating that the side chain in the vicinity of the catalytic residue Ser222 affects the catalytic rate constant.

The crystal structure of zinc-containing ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7

The crystal structure of ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7 was determined by multiple isomorphous replacement supplemented with anomalous scattering effects of iron atoms in the Fe-S clusters, and refined at 2.0 A resolution to a crystallographic R value of 0.173. The structural model contains a polypeptide chain of 103 amino acid residues, 2 [3Fe-4S] clusters, and 31 water molecules; in this model, the cluster corresponding to cluster II in bacterial dicluster ferredoxins loses the fourth iron atom although it may originally be a [4Fe-4S] cluster. The structure of the archaeal ferredoxin consists of two parts: the core fold part (residues 37-103) and the N-terminal extension part (residues 1-36). The "core fold" part has an overall main-chain folding common to bacterial dicluster ferredoxins, containing two clusters as the active center, two alpha-helices near the clusters, and two sheets of two-stranded antiparallel beta-sheet (the terminal and central beta-sheets). The "N-terminal extension" part is mainly formed by a one-turn alpha-helix and a three-stranded antiparallel beta-sheet. The beta-sheet in the N-terminal extension is hydrogen-bonded with the terminal beta-sheet in the core fold to form a larger beta-sheet. The distinct structural feature of this archaeal ferredoxin lies in the zinc-binding center where the zinc ion is tetrahedrally ligated by four amino acid residues (His 16, His 19, and His 34 from the N-terminal extension, and Asp 76 from the core fold). The zinc ion in the zinc-binding center is located at the interface between the core fold and the N-terminal extension, and connects the beta-sheet in the N-terminal extension and the central beta-sheet in the core fold through the zinc ligation. Thus, the zinc ion plays an important role in stabilizing the structure of the present archaeal ferredoxin by connecting the N-terminal extension and the core fold, which may be common to thermoacidophilic archaeal ferredoxins.

Molecular and phylogenetic characterization of isopropylmalate dehydrogenase of a thermoacidophilic archaeon, Sulfolobus sp. strain 7

The archaeal leuB gene encoding isopropylmalate dehydrogenase of Sulfolobus sp. strain 7 was cloned, sequenced, and expressed in Escherichia coli. The recombinant Sulfolobus sp. enzyme was extremely stable to heat. The substrate and coenzyme specificities of the archaeal enzyme resembled those of the bacterial counterparts. Sedimentation equilibrium analysis supported an earlier proposal that the archaeal enzyme is homotetrameric, although the corresponding enzymes studied so far have been reported to be dimeric. Phylogenetic analyses suggested that the archaeal enzyme is homologous to mitochondrial NAD-dependent isocitrate dehydrogenases (which are tetrameric or octameric) as well as to isopropylmalate dehydrogenases from other sources. These results suggested that the present enzyme is the most primitive among isopropylmalate dehydrogenases belonging in the decarboxylating dehydrogenase family.

2-oxoacid:ferredoxin oxidoreductase from the thermoacidophilic archaeon, Sulfolobus sp. strain 7

The purified 2-oxoacid:ferredoxin oxidoreductase of a thermoacidophilic and aerobic crenarchaeote, Sulfolobus sp. strain 7, consists of 70-kDa alpha and 37-kDa beta subunits, and contains one thiamine pyrophosphate (TPP), one [4Fe-4S]2+.1+ cluster, and two magnesium atoms per alpha beta structure. It exhibits a broad substrate specificity toward 2-oxoacids such as 2-oxoglutarate, 2-oxobutyrate, and pyruvate. The gene encoding the archaeal oxidoreductase was cloned, and the two open reading frames encoding the alpha (632 amino acids) and beta subunits (305 amino acids), respectively, were sequenced. Careful sequence alignment revealed several consensus motifs of this enzyme family, as well as possible cofactor binding residues of the Sulfolobus enzyme. This new structural information also indicates that (i) several genetic fusions and reorganization of the early, possibly alpha beta gamma delta-type enzyme similar to those from hyperthermophiles have taken place during evolution of the 2-oxoacid:ferredoxin (flavodoxin) oxidoreductase superfamily, which might have occurred in different ways in early aerobic archaea and early anaerobic bacteria, and that (ii) enzymes with different subunit compositions should have an essentially similar catalytic mechanism with one TPP and at least one [4Fe-4S] cluster as the minimal set of redox centers.

Molecular cloning, sequencing, and heterologous expression of a novel zinc-containing ferredoxin gene from a thermoacidophilic Archaeon Sulfolobus sp. strain 7

The gene encoding a novel zinc-containing ferredoxin from a hyperthermophilic and acidophilic archaeon (archaebacterium) Sulfolobus sp. strain 7 was cloned and sequenced. The DNA sequence predicts a 103 residue protein after removal of N-terminal methionine, which is in good agreement with the results of the protein analysis. Surprisingly, the residues responsible for binding a zinc atom were conserved among three other thermoacidophilic archaea. A common sequence stretch VXGXHXGHX8-17PXXLGXHGTX38-56KXDPV is proposed as a new zinc-binding motif, where three histidines and an aspartic acid are ligated to a zinc atom. The ferredoxin gene was expressed in Eschericia coli. The recombinant ferredoxin was indistinguishable from the protein purified from Sulfolobus sp. strain 7 cells by several criteria so far investigated except that the methylation of the 29th lysine was suppressed.

Resolution of the aerobic respiratory system of the thermoacidophilic archaeon, Sulfolobus sp. strain 7. II. Characterization of the archaeal terminal oxidase subcomplexes and implication for the intramolecular electron transfer

The terminal segment of the aerobic respiratory chain of the thermoacidophilic archaeon Sulfolobus sp. strain 7 is an unusual caldariellaquinol oxidase supercomplex, which contains at least one b-type and three spectroscopically distinguishable a-type cytochromes, one copper, and a Rieske-type FeS center. In this paper, we report the purification and characterization of two different forms of the archaeal a-type cytochromes, namely, a three-subunit cytochrome a583-aa3 subcomplex and a single-subunit cytochrome aa3 derived from the cytochrome subcomplex, in order to facilitate further studies on the terminal oxidase segment of Sulfolobus. The optical and EPR spectroscopic analyses suggest the presence of two different low-spin heme centers and one high-spin heme center in the purified cytochrome a583-aa3 subcomplex, and one low-spin and one high-spin hemes in cytochrome aa3, respectively. The Rieske-type FeS center detected in the purified cytochrome supercomplex was absent in two forms of the a-type cytochrome oxidase, indicating its association with cytochrome b562. The crystal field parameters of the lowspin heme a583 center indicate that its axial ligands may be similar to those of cytochromes c, rather than conventional bis-histidine ligation. In spite of the absence of any c-type cytochrome, a ferrocytochrome c oxidase activity was detected in the archaeal purified cytochrome a583-aa3 subcomplex with no quinol oxidase activity, but not in the purified cytochrome oxidase supercomplex, which has been tentatively interpreted as a representative of electron transfer from the Rieske FeS center to cytochrome a583 in vivo. Thus, our results indicate the following scheme for the intramolecular electron transfer of the terminal oxidase supercomplex from Sulfolobus sp. strain 7: [caldariellaquinol-->] b562-->Rieske FeS center-->a583 aa3-->molecular oxygen.

Resolution of the aerobic respiratory system of the thermoacidophilic archaeon, Sulfolobus sp. strain 7. III. The archaeal novel respiratory complex II (succinate:caldariellaquinone oxidoreductase complex) inherently lacks heme group

An active respiratory complex II (succinate:quinone oxidoreductase) has been purified from tetraether lipid membranes of the thermoacidophilic archaeon, Sulfolobus sp. strain 7. It consists of four different subunits with apparent molecular masses of 66, 37, 33, and 12 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The 66-kDa subunit contains a covalently bound flavin, the 37-kDa subunit is a possible iron-sulfur protein carrying three distinct types of EPR-visible FeS cluster, and the 33- and 12-kDa subunits are putative membrane-anchor subunits, respectively. While no heme group is detected in the purified complex II, it catalyzes succinate-dependent reduction of ubiquinone-1 and 2,6-dichlorophenolindophenol in the absence of phenazine methosulfate. The respiratory complex II of Sulfolobus sp. strain 7 appears to be novel in that it functions as a true succinate:caldariellaquinone oxidoreductase, although inherently lacking any heme group. This further indicates that the heme group of several respiratory complexes II may not be involved in the redox intermediates of the electron transfer from succinate to quinone.

Purification and characterization of 3-isopropylmalate dehydrogenase from a thermoacidophilic archaebacterium Sulfolobus sp. strain 7

3-Isopropylmalate dehydrogenase was purified (about 2000-fold) to homogeneity for the first time from an archaebacterium, Sulfolobus sp. strain 7. The enzyme showed an apparent molecular mass of about 110 kDa by gel filtration and a single 36-kDa polypeptide band on SDS-PAGE, suggesting tri- or tetrameric structure. The pI value was 6.9. The N-terminal amino acid sequence was similar to enzymes from other sources. The enzyme activity was greatly stimulated by the presence of Mn2+, Cd2+, Mg2+, or Co2+. In contrast to 3-isopropylmalate dehydrogenase from other sources, monovalent cations such as K+ and Na+ were neither essential for activity nor stability of the protein. The enzyme was extraordinarily thermostable.

Ferredoxin-dependent redox system of a thermoacidophilic archaeon, Sulfolobus sp. strain 7. Purification and characterization of a novel reduced ferredoxin-reoxidizing iron-sulfur flavoprotein

To elucidate the ferredoxin-dependent redox system of the thermoacidophilic, aerobic archaeon Sulfolobus sp. strain 7, a novel FeS flavoprotein, which can reoxidize the reduced 7Fe ferredoxin in vitro, has been purified and characterized (designated as IFP) using the cognate 7Fe ferredoxin and 2-oxoacid:ferredoxin oxidoreductase, a key enzyme of the archaeal tricarboxylic acid cycle. IFP consists of three non-identical subunits with apparent molecular masses of 87, 32, and 22 kDa, respectively, and contains at least two FMN (Em, 6.8 = -57 mV) and two plant-ferredoxin-type [2Fe-2S]2+,1+ clusters (Em, 6.8 = -260 mV)/alpha 2 beta 2 gamma 2 structure. Both FeS and flavin centers of IFP are slowly but fully reduced by the enzymatically reduced cognate ferredoxin under anaerobic conditions at 50 degrees C, but not by NAD(P)H. Thus, the ferredoxin-dependent redox system of Sulfolobus sp. strain 7 is tentatively proposed as follows: 2-oxoacid:ferredoxin oxidoreductase (thiamine pyrophosphate and [4Fe-4S] cluster)-->ferredoxin-->IFP ([2Fe-2S] cluster-->FMN).

Alternative form of the dicluster ferredoxin from the thermoacidophilic archaeon, Sulfolobus sp. strain 7

An alternative form of a 7Fe dicluster-type ferredoxin (Fd-B) with a different charge density was purified as a minor component from the aerobic and thermoacidophilic archaeon, Sulfolobus sp. strain 7. Comparison of its properties with those of native 7Fe ferredoxin (Fd-A), a major ferredoxin, was made in terms of the molecular properties, the absorption, circular dichroism and electron paramagnetic resonance spectral properties, and the reactivity coupled with the cognate 2-oxoacid:ferredoxin oxidoreductase at 50 degrees C. Our results suggest that the Sulfolobus 7Fe ferredoxin has two spectroscopically distinct forms with slightly different conformations.

Functional and evolutionary implications of a [3Fe-4S] cluster of the dicluster-type ferredoxin from the thermoacidophilic archaeon, Sulfolobus sp. strain 7

The dicluster-type ferredoxin is a key electron carrier in the cytoplasm of the aerobic and thermoacidophilic archaeon, Sulfolobus sp. strain 7, and contains 1 aspartate and 7 cysteine residues as possible ligands to two FeS clusters. The optical, electron paramagnetic resonance (EPR), and cyclic voltammetric studies suggest the presence of one each of [3Fe-4S]1+,0 (-280 mV) and [4Fe-4S]2+,1+ (-530 mV) clusters in the purified Sulfolobus ferredoxin, and the lower potential [4Fe-4S] center was scarcely reducible by excess dithionite even at pH 9. While the Sulfolobus ferredoxin has been known to function as an electron acceptor of 2-oxoacid:ferredoxin oxidoreductase (Kerscher, L., Nowitzki, S., and Oesterhelt, D. (1982) Eur. J. Biochem. 128, 223-230), it is not known whether one or both of two clusters is reduced during the steady-state turnover of the enzyme. Here we show by combinations of the optical and EPR spectroscopies that only the higher potential [3Fe-4S] cluster is reduced at the physiological pH during the steady-state turnover of the purified 2-oxoacid:ferredoxin oxidoreductase at 50 degrees C. The functional significance and evolutionary implications of the [3Fe-4S] center in dicluster-type ferredoxins are discussed.

Hydrophobic interaction at the subunit interface contributes to the thermostability of 3-isopropylmalate dehydrogenase from an extreme thermophile, Thermus thermophilus

We cloned and sequenced the leuB gene encoding 3-isopropylmalate dehydrogenase from Escherichia coli K-12 (JM103). Errors (33 residues) were found and corrected in the sequence previously reported for the leuB gene of Thermus thermophilus. The three-dimensional structure of the thermophile enzyme and the amino acid sequence comparison suggested that a part of the high stability of the T. thermophilus enzyme is conferred by increased hydrophobic interaction at the subunit-subunit interface. Two residues at the interface of the T. thermophilus enzyme, Leu246 and Val249, are substituted with less hydrophobic residues, Glu and Met, respectively, in the E. coli enzyme, whereas other residues in this region are highly conserved. The mutated T. thermophilus enzyme [L246E, V249M]IPMDH had reduced stability to heat. Two residues of the E. coli dehydrogenase, Glu256 and Met259, were replaced with the corresponding residues from the thermophile sequence. The resulted mutant enzyme was more resistant to heat than the wild-type enzyme.

An ecto-enzyme from Sulfolobus acidocaldarius strain 7 which catalyzes hydrolysis of inorganic pyrophosphate, ATP, and ADP: purification and characterization

Membranes of Sulfolobus acidocaldarius, a thermoacidophilic archaebacterium, show novel enzymatic activities to hydrolyze PPi, ATP, and ADP at an optimal pH of 3, equal to the growth optimum. The activity increased by about 2-fold on addition of PPi and/or Pi to the growth medium, when yeast extract and casamino acids were removed. The enzyme which hydrolyzes PPi at pH 3 was solubilized and purified by successive chromatographies. The final preparation showed a 26 kDa single band on SDS-PAGE, and a molecular mass of 35 kDa on gel permeation chromatography. The Km and Vmax for PPi were 0.16 mM and 33 mumol Pi released/min/mg at 55 degrees C. ATP and ADP were also good substrates. Divalent cations were not essential for activity. Substrate inhibition at more than 5 mM PPi, ATP or ADP was observed. AMP, glucose-6-phosphate, and p-nitrophenyl phosphate were not hydrolyzed at all. The activity was 4-fold stimulated by addition of the lipid fraction extracted from the organism.

MELAS without ragged red fibers or lactic acidosis diagnosed by mitochondrial DNA testing

A case of mitochondrial encephalomyopathy with lactic acidosis, a stroke-like episode (MELAS) without ragged red fiber, diagnosed by mitochondrial DNA testing, is reported. A 37-year-old woman experienced a sudden and recurrent headache with vomiting and stroke-like episodes. Brain CT and MRI showed multiple infarction in the temporal lobes, not corresponding to artery distribution. However, the plasma levels of lactate and pyruvate were normal, and showed no increased after aerobic exercise. Biopsied muscle showed no evidence of ragged red fibers and deficient activity of mitochondrial enzymes in the respiratory chain. The final diagnosis was made by mitochondrial DNA testing. A southern blot analysis after Apa I digestion revealed the A-to-G mutation in the tRNA(Leu(UUR)), which is specific to MELAS.

An extremely stable inorganic pyrophosphatase purified from the cytosol of a thermoacidophilic archaebacterium, Sulfolobus acidocaldarius strain 7

A highly active inorganic pyrophosphatase was purified to electrophoretical homogeneity from the cytosol of Sulfolobus acidocaldarius strain 7, an extremely thermoacidophilic archaebacterium. The enzyme has an apparent molecular mass of 80 kDa as estimated by gel permeation chromatography, and showed a 21-kDa polypeptide on SDS-PAGE, suggesting that the archaebacterial enzyme is similar to most of the eubacterial pyrophosphatases rather than eukaryotic ones. The pI = 5.1. The enzyme showed relatively high content of Pro and low content of Ser plus Thr. The optimal pH was 6.5 (at 56 degrees C). From the Arrhenius plot an activation energy of 11.2 kcal/mol was obtained between 37-95 degrees C. The specific activity was 617 mumol Pi release min-1 mg-1 at 56 degrees C. The S. acidocaldarius pyrophosphatase was extremely stable. Complete activity remained after incubation at 100 degrees C for 10 min. No dissociation into subunit or unfolding of polypeptide chain occurred in the presence of 8 M urea. Experiments using guanidine-HCl suggested that the transition between a native tetrameric state and an unfolded state is completely reversible, and essentially independent of any additional factors such as divalent metal cation or dithiothreitol.

Molecular cloning of the isocitrate dehydrogenase gene of an extreme thermophile, Thermus thermophilus HB8

The gene coding for isocitrate dehydrogenase of an extreme thermophile, Thermus thermophilus HB8, was cloned and sequenced. This gene consists of a single open reading frame of 1,485 bp preceded by a Shine-Dalgarno ribosome binding site. Promoter- and terminatorlike sequences were detected upstream and downstream of the open reading frame, respectively. The G + C content of the coding region was 65.6%, and that of the third nucleotide of the codons was 90.3%. On the basis of the deduced amino acid sequence, the Mr of the monomeric enzyme was calculated as 54,189, an Mr which is similar to that of the purified protein determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. A comparison of the amino acid sequence of the T. thermophilus enzyme with that of the Escherichia coli enzyme showed (i) a 37% overall similarity; (ii) the conservation of the Ser residue, which is known to be phosphorylated in the E. coli enzyme, and of the surrounding sequence; and (iii) the presence of 141 extra residues at the C terminus of the T. thermophilus enzyme. T. thermophilus isocitrate dehydrogenase showed a high sequence homology (33% of the amino acid sequence is identical) to isopropylmalate dehydrogenase from the same organism and was suggested to have evolved from a common ancestral enzyme.

Crystallization and preliminary X-ray studies on Sulfolobus acidocaldarius ferredoxin

Ferredoxin from a thermoacidophilic archaebacterium, Sulfolobus acidocaldarius, has been crystallized. The space group is P4(3)2(1)2 or P4(1)2(1)2 and the cell dimensions are a = b = 50.12 A and c = 69.52 A. The Vm value is calculated to be 1.88 A3/Da, assuming one molecule per asymmetric unit. The crystal diffracts X-rays beyond 2.0 A resolution.

Archaebacterial ATPases: relationship to other ion-translocating ATPase families examined in terms of immunological cross-reactivity

Immunological cross-reactivity among three types of H(+)-ATPases, that is, three archaebacterial ATPases, the F1-ATPase from thermophilic bacterium PS3 (TF1) and the vacuolar membrane ATPase from Saccharomyces cerevisiae, was examined by means of immunoblot analyses. The three archaebacterial ATPases were very similar in immunological cross-reactivity, suggesting that they belong to the same family of ATPases. Cross-reaction was also observed between the ATPase from Sulfolobus acidocaldarius, one of the three archaebacteria, and TF1. S. cerevisiae vacuolar ATPase reacted with the antibodies prepared against each of the three archaebacterial ATPases, but did not react with the antibody against TF1. Electron microscopic examination revealed that the oligomeric structure of Sulfolobus ATPase was very similar to that of F1-ATPase. These results, taken together, suggest that the archaebacterial ATPases share close structural similarities with the vacuolar ATPases, and, to a lesser degree, with the F0F1-ATPases.

A novel a-type terminal oxidase from Sulfolobus acidocaldarius with cytochrome c oxidase activity

Cytochrome C oxidase was solubilized with a nonionic detergent n-decanoyl-N-methyl glucamide from the membranes of Sulfolobus acidocaldarius, a thermoacidophilic archaebacterium, and was purified. The enzyme oxidized horse heart cytochrome C with a Vmax of 63 mumols/min/mg at 50 degrees C. The activity was sensitive to cyanide. The enzyme also catalyzed oxygen uptake detergent on N, N, N', N'-tetramethyl p-phenylene diamine. An apparent molecular mass was estimated to be 150 kDa. The enzyme is composed of three subunits of 37, 23 and 14 kDa. Spectral characteristics were similar to typical bacterial aa3 except for the presence of a novel 583 nm peak observed in reduced minus oxidized difference spectrum.

A highly stable NADP-dependent isocitrate dehydrogenase from Thermus thermophilus HB8: purification and general properties

NADP-dependent isocitrate dehydrogenase (EC 1.1.1.42) was purified to electrophoretic homogeneity from an extremely thermophilic bacterium, Thermus thermophilus HB8, and shown to be a dimeric protein of molecular weight 115,000, with a pI of 5.5. The amino acid composition of the present enzyme was similar to that reported for other bacterial counterparts, except for a high Arg/Lys ratio and a low Cys content. Divalent cations, such as Mn2+ and Mg2+, were essential for activity. The optimal pH was 7.8 at 55 degrees C. The Km values for NADP and D-isocitrate were 6.3 and 8.8 microM, respectively, with a Vmax of 77.6 mumol/min per mg at 55 degrees C. NAD was able to replace NADP with low efficiency. Backward reaction at 40 degrees C indicated that the Km value for 2-oxoglutarate was 63 microM with a Vmax of 4% that of the forward reaction at that temperature. The enzyme was highly stable against high temperature and denaturing reagents.

Purification and properties of the ATPase solubilized from membranes of an acidothermophilic archaebacterium, Sulfolobus acidocaldarius

A novel ATPase was solubilized from membranes of an acidothermophilic archaebacterium, Sulfolobus acidocaldarius, with low ionic strength buffer containing EDTA. The enzyme was purified to homogeneity by hydrophobic chromatography and gel filtration. The molecular weight of the purified enzyme was estimated to be 360,000. Polyacrylamide gel electrophoresis of the purified enzyme in the presence of sodium dodecyl sulfate revealed that it consisted of three kinds of subunits, alpha, beta, and gamma, whose molecular weights were approximately 69,000, 54,000, and 28,000, respectively, and the most probable subunit stoichiometry was alpha 3 beta 3 gamma 1. The purified ATPase hydrolyzed ATP, GTP, ITP, and CTP but not UTP, ADP, AMP, or p-nitrophenylphosphate. The enzyme was highly heat stable and showed an optimal temperature of 85 degrees C. It showed an optimal pH of around 5, very little activity at neutral pH, and another small activity peak at pH 8.5. The ATPase activity was significantly stimulated by bisulfite and bicarbonate ions, the optimal pH remaining unchanged. The Lineweaver-Burk plot was linear, and the Km for ATP and the Vmax were estimated to be 1.6 mM and 13 mumol Pi.mg.-1.min-1, respectively, at pH 5.2 at 60 degrees C in the presence of bisulfite. The chemical modification reagent, 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole, caused inactivation of the ATPase activity although the enzyme was not inhibited by N,N'-dicyclohexylcarbodiimide, N-ethyl-maleimide, azide or vanadate. These results suggest that the ATPase purified from membranes of S. acidocaldarius resembles other archaebacterial ATPases, although a counterpart of the gamma subunit has not been found in the latter. The relationship of the S. acidocaldarius ATPase to other ion-transporting ATPases, such as F0F1 type or E1E2 type ATPases, was discussed.

Purification and properties of NADH dehydrogenase from a thermoacidophilic archaebacterium, Sulfolobus acidocaldarius

An NADH dehydrogenase was purified to electrophoretical homogeneity from Sulfolobus acidocaldarius, a thermoacidophilic archaebacterium optimally growing at pH 2-3 and 75 degrees C. A 2,100-fold purification was achieved. The purified enzyme is an acidic protein with an isoelectric point of 5.6 and a molecular weight of 95,000, consisting of two 50,000-dalton subunits. The enzyme showed an absorption spectrum characteristic of flavoproteins, with maxima at 272, 372, and 448 nm. The enzyme is highly thermostable, is specific for NADH as an electron donor, and is capable of using 2,6-dichlorophenolindophenol, ferricyanide, benzoquinone, and naphthoquinone as electron acceptors. Though at a low rate, caldariellaquinone, a unique and sole benzothiophenequinone in the genus Sulfolobus, was also reduced by the enzyme, suggesting that the enzyme is a possible member of the respiratory chain of the thermoacidophilic archaebacterium.

Membrane-bound ATPase of a thermoacidophilic archaebacterium, Sulfolobus acidocaldarius

The membranes of Sulfolobus, a thermoacidophilic archaebacterium showed two types of ATP hydrolyzing activity. One was that of a neutral ATPase at an optimum pH around 6.5. This enzyme was activated by 10 mM sulfate with a shift of optimum pH to 5. In these respects, the enzyme was similar to membrane-bound ATPase of Thermoplasma, another thermoacidophilic archaebacterium, reported by Searcy and Whatley [1982) Zbl. Bakt. Hyg., I. Abt. Orig. C3, 245-257). The enzyme hydrolyzed ATP and other NTPs, but not ADP or AMP. It was highly thermostable, but irreversibly inactivated in 0.1 M HCl. The other activity was that of an acidic apyrase at an optimum pH around 2.5. This enzyme was extremely stable toward high temperature and acid and inhibited by sulfate. Both of these ATP hydrolyzing enzymes were resistant to N,N'-dicyclohexylcarbodiimide (DCCD), azide, oligomycin, N'-ethylmaleimide, p-chloromercuribenzoate, orthovanadate, or ouabain. Sulfolobus ATPases differ from F1 and other transport ATPases so far described.

Detection of the conformational change in the catalytic site of adenosine triphosphatase from beef liver mitochondria by affinity labeling with the dialdehyde derivative of ethenoadenosine triphosphate

Beef liver mitochondrial F1ATPase was inactivated by the 2',3'-dialdehyde derivative of ethenoATP (epsilon ATP) in a pseudo-first order reaction. The kinetics of protection of the enzyme against inactivation by various nucleoside triphosphates (NTPs) revealed that the dial-epsilon ATP was bound to the catalytic site as an affinity label. Certain anions (sulfate or bicarbonate) were ineffective for protection. In the early phase of the reaction, inactivation was due to the binding of 1 mol dial-epsilon ATP per mol enzyme. In this phase, dial-epsilon ATP bound exclusively to the subunit beta of the enzyme, indicating that the catalytic site is in this subunit. The fluorescence of the ethenoadenosine moiety, bound exclusively to the subunit beta of the enzyme, was measured as a conformational probe of the catalytic site region. Addition of ATP or CTP to the labeled enzyme resulted in a decrease in the fluorescence intensity. GTP and other NTPs were less effective than ATP or CTP. The anions (sulfate of bicarbonate) suppressed the ability of ATP to decrease the fluorescence in a competitive manner. Quantitative analysis of these fluorescence changes suggested that they might originate from the binding of the NTP to the regulatory site of the enzyme. These findings are in good agreement with the two-site model proposed by us (Wakagi, T. & Ohta, T. (1981) J. Biochem. 89, 1205) which was deduced from the steady state kinetics of the NTPase reactions catalyzed by the F1ATPase.

Implications of the existence of two states of beef liver mitochondrial adenosine triphosphatase as revealed by kinetic studies

The results of studies on the initial velocity in hydrolysis reactions of ATP and other nucleoside triphosphates with beef liver mitochondrial ATPase can be summarized as follows. 1. Double reciprocal plots of substrate concentration vs. initial velocity were linear for all the nucleoside triphosphates tested except for ATP, which showed a negative cooperativity. 2. Bicarbonate ion increased the rate of ATP hydrolysis and diminished its negative cooperativity, whereas hydrolysis of other nucleoside triphosphates was only slightly affected by the anion. 3. An excess of nucleoside triphosphate apparently inhibited its own hydrolysis for all kinds of nucleoside triphosphates tested, whereas an excess of magnesium ion apparently inhibited only ATP hydrolysis. 4. Inhibition of ATPase activity with an excess of magnesium ion was no longer observed when the reaction was carried out at low temperature (10 degrees C) or in the presence of sulfate. Under these conditions, the kinetics of ATP hydrolysis were apparently of simple Michaelis-Menten type. These observations suggest the existence of two states ("A" and "N") of beef liver mitochondrial ATPase. The state "A" is characterized by phenomena specifically affecting ATP hydrolysis, such as the inhibition by excess magnesium ion, and the negatively cooperative profile in the dose-response curve of ATP. In the state "N" proceed the hydrolysis reactions of other nucleoside triphosphates and of ATP under limited conditions. The two states ("A" and "N") can be related to an enzyme model with a catalytic site and a regulatory site. Computer stimulation revealed that such a model could account well for the experimental data.